import_qiime_sample_data: Import just 'sample_data' file from QIIME pipeline.
In phyloseq: Handling and analysis of high-throughput microbiome census data

Description Usage Arguments Details Value See Also Examples

QIIME produces several files that can be analyzed in the phyloseq-package, This includes the map-file, which is an important input to QIIME that can also indicate sample covariates. It is converted naturally to the sample_data component data type in phyloseq-package, based on the R data.frame.

1	import_qiime_sample_data(mapfilename)

mapfilename

(Required). A character string or connection. That is, any suitable file argument to the read.table function. The name of the QIIME map file required for processing pyrosequencing tags in QIIME as well as some of the post-clustering analysis. This is a required input file for running QIIME. Its strict formatting specification is expected by this function, do not attempt to modify it manually once it has worked properly in QIIME.

See import_qiime for more information about QIIME. It is also the suggested function for importing QIIME-produced data files.

A sample_data object.

import

merge_phyloseq

phyloseq

import_qiime

import_qiime_otu_tax

import_env_file

1 2	mapfile <- system.file("extdata", "master_map.txt", package = "phyloseq") import_qiime_sample_data(mapfile)

Sample Data:        [28 samples by 7 sample variables]:
         X.SampleID  Primer Final_Barcode Barcode_truncated_plus_T
CL3             CL3 ILBC_01        AACGCA                   TGCGTT
CC1             CC1 ILBC_02        AACTCG                   CGAGTT
SV1             SV1 ILBC_03        AACTGT                   ACAGTT
M31Fcsw     M31Fcsw ILBC_04        AAGAGA                   TCTCTT
M11Fcsw     M11Fcsw ILBC_05        AAGCTG                   CAGCTT
F11Fcsw     F11Fcsw ILBC_06        AATCAG                   CTGATT
M31Plmr     M31Plmr ILBC_07        AATCGT                   ACGATT
M11Plmr     M11Plmr ILBC_08        ACACAC                   GTGTGT
F21Plmr     F21Plmr ILBC_09        ACACAT                   ATGTGT
M31Tong     M31Tong ILBC_10        ACACGA                   TCGTGT
M11Tong     M11Tong ILBC_11        ACACGG                   CCGTGT
F11Tong     F11Tong ILBC_12        ACACTA                   TAGTGT
LMEpi24M   LMEpi24M ILBC_13        ACACTG                   CAGTGT
SLEpi20M   SLEpi20M ILBC_15        ACAGAG                   CTCTGT
AQC1cm       AQC1cm ILBC_16        ACAGCA                   TGCTGT
AQC4cm       AQC4cm ILBC_17        ACAGCT                   AGCTGT
AQC7cm       AQC7cm ILBC_18        ACAGTG                   CACTGT
NP2             NP2 ILBC_19        ACAGTT                   AACTGT
NP3             NP3 ILBC_20        ACATCA                   TGATGT
NP5             NP5 ILBC_21        ACATGA                   TCATGT
TRRsed1     TRRsed1 ILBC_22        ACATGT                   ACATGT
TRRsed2     TRRsed2 ILBC_23        ACATTC                   GAATGT
TRRsed3     TRRsed3 ILBC_24        ACCACA                   TGTGGT
TS28           TS28 ILBC_25        ACCAGA                   TCTGGT
TS29           TS29 ILBC_26        ACCAGC                   GCTGGT
Even1         Even1 ILBC_27        ACCGCA                   TGCGGT
Even2         Even2 ILBC_28        ACCTCG                   CGAGGT
Even3         Even3 ILBC_29        ACCTGT                   ACAGGT
         Barcode_full_length         SampleType
CL3              CTAGCGTGCGT               Soil
CC1              CATCGACGAGT               Soil
SV1              GTACGCACAGT               Soil
M31Fcsw          TCGACATCTCT              Feces
M11Fcsw          CGACTGCAGCT              Feces
F11Fcsw          ACGAGACTGAT              Feces
M31Plmr          CGAGTCACGAT               Skin
M11Plmr          GCCATAGTGTG               Skin
F21Plmr          GTAGACATGTG               Skin
M31Tong          TGTGGCTCGTG             Tongue
M11Tong          TAGACACCGTG             Tongue
F11Tong          CGGATCTAGTG             Tongue
LMEpi24M         CATGAACAGTG         Freshwater
SLEpi20M         AGCCGACTCTG         Freshwater
AQC1cm           GACCACTGCTG Freshwater (creek)
AQC4cm           CAAGCTAGCTG Freshwater (creek)
AQC7cm           ATGAAGCACTG Freshwater (creek)
NP2              TCGCGCAACTG              Ocean
NP3              GCTAAGTGATG              Ocean
NP5              GAACGATCATG              Ocean
TRRsed1          CACGTGACATG Sediment (estuary)
TRRsed2          TGCGCTGAATG Sediment (estuary)
TRRsed3          GATGTATGTGG Sediment (estuary)
TS28             GCATCGTCTGG              Feces
TS29             CTAGTCGCTGG              Feces
Even1            TGACTCTGCGG               Mock
Even2            TCTGATCGAGG               Mock
Even3            AGAGAGACAGG               Mock
                                          Description
CL3          Calhoun South Carolina Pine soil, pH 4.9
CC1          Cedar Creek Minnesota, grassland, pH 6.1
SV1        Sevilleta new Mexico, desert scrub, pH 8.3
M31Fcsw       M3, Day 1, fecal swab, whole body study
M11Fcsw      M1, Day 1, fecal swab, whole body study 
F11Fcsw     F1, Day 1,  fecal swab, whole body study 
M31Plmr       M3, Day 1, right palm, whole body study
M11Plmr      M1, Day 1, right palm, whole body study 
F21Plmr     F1, Day 1,  right palm, whole body study 
M31Tong          M3, Day 1, tongue, whole body study 
M11Tong          M1, Day 1, tongue, whole body study 
F11Tong          F1, Day 1, tongue, whole body study 
LMEpi24M Lake Mendota Minnesota, 24 meter epilimnion 
SLEpi20M Sparkling Lake Wisconsin, 20 meter eplimnion
AQC1cm                   Allequash Creek, 0-1cm depth
AQC4cm                  Allequash Creek, 3-4 cm depth
AQC7cm                  Allequash Creek, 6-7 cm depth
NP2            Newport Pier, CA surface water, Time 1
NP3            Newport Pier, CA surface water, Time 2
NP5            Newport Pier, CA surface water, Time 3
TRRsed1                Tijuana River Reserve, depth 1
TRRsed2                Tijuana River Reserve, depth 2
TRRsed3                Tijuana River Reserve, depth 2
TS28                                          Twin #1
TS29                                          Twin #2
Even1                                           Even1
Even2                                           Even2
Even3                                           Even3